Find Corresponding GenBank ID

Question

[Penny Liu]

This is what I have.

• BioSample Accession: SAMN04492225

• BioProject Accession: PRJNA312015

Is it possible to get corresponding GenBank ID via BioSample or BioProject Accession? It is great if you guys could give me some valuable suggestions and comments how to solve.

Thanks

[GenoMax]

Are you referring to NZ* accession numbers or WP* Protein ID's as described on this summary annotation page?

[Penny Liu]

Thanks, but it's not what I expected. For example, https://www.ncbi.nlm.nih.gov/protein/AAC76128.2

BioProject: PRJNA225, BioSample: SAMN02604091. Both of these should refer to the GenBank accession AAC76128.

[GenoMax]

I am not sure I understand your intent. You want to associate a biosample (which is whole genome sequence) to a specific protein?

[Penny Liu]

I was assigned BioProject and BioSample accession number when I take WGS submission. Will I get the GenBank ID when the annotation process is finished? Perhaps I misunderstood and thanks again!

[GenoMax]

Referring back to the original example isn't GCA_002318995.1the accession that has been assigned to your genome? Looks like yours is one of the 8 assemblies available for this organism.

[Penny Liu]

In my submission, the strain is KCT instead of YHL.

[GenoMax]

Classification is at the taxid level so it looks like all strains of the species are collected under main taxid (Shewanella algae (taxid:38313)).

[Penny Liu]

As far as I know, Shewanella haliotis and Shewanella algae are the same genus but different species.

[Tanvir Ahamed]

I did this as a part of one of my project. This could be helpful

library("genomes")
proks <- reports("prokaryotes.txt")

# BioProject Accession: PRJNA312015
biopro <- proks[grep("312015",proks$`BioProject ID`),]
ftp_biopro <- biopro$`FTP Path`


file_type <- "feature_table.txt"
GCA <- tail(unlist(strsplit(ftp_biopro, "/")),1)
file_type <- paste0(GCA,"_",paste0(file_type, ".gz"))
down_file <- paste(ftp_biopro,file_type, sep ="/")
dest <- "weather.op.gz" 
download.file(url = down_file, destfile = dest) 
my_data <- read.table(dest, header=F, sep = "\t")